15 research outputs found
Human RECQL5 helicase; A Target Enabling Package
<p>RECQL5 is a member of the RecQ family of helicase which have important functions in DNA repair pathways and maintenance of genome integrity. RECQL5 has recently been identified as a synthetic lethal candidate in various haematological malignancies and has been verified by knockdown to sensitize myeloproliferative neoplasms (MPN) to DNA damaging agents. In this TEP we have expressed purified and determined the first ever crystal structures of RECQL5, in both APO and ADP/Mg2+ bound forms which crystallize in two distinctly different conformations. In vitro DNA stimulated ATPase assays suitable for high throughput screening have been developed as well as lower throughput orthogonal assays to verify potential hits. A fragment screening campaign has been initiated and single fragment hit has identified a potential allosteric site that may be targeted to block the transition between conformations that it thought to be part of the helicase mechanism. Finally included as part of the package we present 3 validated RECQL5 binding nanobodies, one of which is a potent inhibitor of RECQL5 ATPase activity and is suitable for use as a tool reagent to investigate inhibition of RECQL5 and its complexes in vitro.</p
Human RECQL5 helicase; A Target Enabling Package
<p>RECQL5 is a member of the RecQ family of helicase which have important functions in DNA repair pathways and maintenance of genome integrity. RECQL5 has recently been identified as a synthetic lethal candidate in various haematological malignancies and has been verified by knockdown to sensitize myeloproliferative neoplasms (MPN) to DNA damaging agents. In this TEP we have expressed purified and determined the first ever crystal structures of RECQL5, in both APO and ADP/Mg2+ bound forms which crystallize in two distinctly different conformations. In vitro DNA stimulated ATPase assays suitable for high throughput screening have been developed as well as lower throughput orthogonal assays to verify potential hits. A fragment screening campaign has been initiated and single fragment hit has identified a potential allosteric site that may be targeted to block the transition between conformations that it thought to be part of the helicase mechanism. Finally included as part of the package we present 3 validated RECQL5 binding nanobodies, one of which is a potent inhibitor of RECQL5 ATPase activity and is suitable for use as a tool reagent to investigate inhibition of RECQL5 and its complexes in vitro.</p
Human RECQL5 helicase; A Target Enabling Package
<p>RECQL5 is a member of the RecQ family of helicase which have important functions in DNA repair pathways and maintenance of genome integrity. RECQL5 has recently been identified as a synthetic lethal candidate in various haematological malignancies and has been verified by knockdown to sensitize myeloproliferative neoplasms (MPN) to DNA damaging agents. In this TEP we have expressed purified and determined the first ever crystal structures of RECQL5, in both APO and ADP/Mg2+ bound forms which crystallize in two distinctly different conformations. In vitro DNA stimulated ATPase assays suitable for high throughput screening have been developed as well as lower throughput orthogonal assays to verify potential hits. A fragment screening campaign has been initiated and single fragment hit has identified a potential allosteric site that may be targeted to block the transition between conformations that it thought to be part of the helicase mechanism. Finally included as part of the package we present 3 validated RECQL5 binding nanobodies, one of which is a potent inhibitor of RECQL5 ATPase activity and is suitable for use as a tool reagent to investigate inhibition of RECQL5 and its complexes in vitro.</p
Type II Inhibitors Targeting CDK2
Kinases can switch between active
and inactive conformations of
the ATP/Mg<sup>2+</sup> binding motif DFG, which has been explored
for the development of type I or type II inhibitors. However, factors
modulating DFG conformations remain poorly understood. We chose CDK2
as a model system to study the DFG in–out transition on a target
that was thought to have an inaccessible DFG-out conformation. We
used site-directed mutagenesis of key residues identified in structural
comparisons in conjunction with biochemical and biophysical characterization
of the generated mutants. As a result, we identified key residues
that facilitate the DFG-out movement, facilitating binding of type
II inhibitors. However, surprisingly, we also found that wild type
CDK2 is able to bind type II inhibitors. Using protein crystallography
structural analysis of the CDK2 complex with an aminopyrimidine-phenyl
urea inhibitor (K03861) revealed a canonical type II binding mode
and the first available type II inhibitor CDK2 cocrystal structure.
We found that the identified type II inhibitors compete with binding
of activating cyclins. In addition, analysis of the binding kinetics
of the identified inhibitors revealed slow off-rates. The study highlights
the importance of residues that may be distant to the ATP binding
pocket in modulating the energetics of the DFG-out transition and
hence inhibitor binding. The presented data also provide the foundation
for a new class of slow off-rate cyclin-competitive CDK2 inhibitors
targeting the inactive DFG-out state of this important kinase target
Type II Inhibitors Targeting CDK2
Kinases can switch between active
and inactive conformations of
the ATP/Mg<sup>2+</sup> binding motif DFG, which has been explored
for the development of type I or type II inhibitors. However, factors
modulating DFG conformations remain poorly understood. We chose CDK2
as a model system to study the DFG in–out transition on a target
that was thought to have an inaccessible DFG-out conformation. We
used site-directed mutagenesis of key residues identified in structural
comparisons in conjunction with biochemical and biophysical characterization
of the generated mutants. As a result, we identified key residues
that facilitate the DFG-out movement, facilitating binding of type
II inhibitors. However, surprisingly, we also found that wild type
CDK2 is able to bind type II inhibitors. Using protein crystallography
structural analysis of the CDK2 complex with an aminopyrimidine-phenyl
urea inhibitor (K03861) revealed a canonical type II binding mode
and the first available type II inhibitor CDK2 cocrystal structure.
We found that the identified type II inhibitors compete with binding
of activating cyclins. In addition, analysis of the binding kinetics
of the identified inhibitors revealed slow off-rates. The study highlights
the importance of residues that may be distant to the ATP binding
pocket in modulating the energetics of the DFG-out transition and
hence inhibitor binding. The presented data also provide the foundation
for a new class of slow off-rate cyclin-competitive CDK2 inhibitors
targeting the inactive DFG-out state of this important kinase target
Human Lysine Demethylase JMJD2D (KDM4D); A Target Enabling Package
<p>There are 4 members of the Lysine Demethylase JMJD2 (KDM4) family. SGC Oxford has expressed, purified and crystallized the catalytic domains of JMJD2A, JMJD2B, JMJD2C and JMJD2D as part of the probe programme. Fragment screening and X-ray crystallography identified a large number of binders, some of which were progressed into a medicinal chemistry programme. Despite significant effort molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p
Human Lysine Demethylase JMJD1B (KDM3B); A Target Enabling Package
<p>There are 3 members of the Lysine Demethylase JMJD1 (KDM3) family, JMJD1A-C. SGC Oxford has expressed, purified and crystallized the catalytic domains of JMJD1A, JMJD1B and JMJD1C as part of the probe programme. Fragment screening and X-ray crystallography identified a large number of binders, some of which were progressed into a medicinal chemistry programme. Despite significant effort molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p
Human Lysine Demethylase JMJD2D (KDM4D); A Target Enabling Package
<p>There are 4 members of the Lysine Demethylase JMJD2 (KDM4) family. SGC Oxford has expressed, purified and crystallized the catalytic domains of JMJD2A, JMJD2B, JMJD2C and JMJD2D as part of the probe programme. Fragment screening and X-ray crystallography identified a large number of binders, some of which were progressed into a medicinal chemistry programme. Despite significant effort molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p
Discovery of a Chemical Tool Inhibitor Targeting the Bromodomains of TRIM24 and BRPF
TRIM24 is a transcriptional regulator
as well as an E3 ubiquitin
ligase. It is overexpressed in diverse tumors, and high expression
levels have been linked to poor prognosis in breast cancer patients.
TRIM24 contains a PHD/bromodomain offering the opportunity to develop
protein interaction inhibitors that target this protein interaction
module. Here we identified potent acetyl-lysine mimetic benzimidazolones
TRIM24 bromodomain inhibitors. The best compound of this series is
a selective BRPF1B/TRIM24 dual inhibitor that bound with a <i>K</i><sub>D</sub> of 137 and 222 nM, respectively, but exerted
good selectivity over other bromodomains. Cellular activity of the
inhibitor was demonstrated using FRAP assays as well as cell viability
data
Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins
The bromodomain and
plant homeodomain finger-containing (BRPF)
family are scaffolding proteins important for the recruitment of histone
acetyltransferases of the MYST family to chromatin. Here, we describe <b>NI-57</b> (<b>16</b>) as new pan-BRPF chemical probe of
the bromodomain (BRD) of the BRPFs. Inhibitor <b>16</b> preferentially
bound the BRD of BRPF1 and BRPF2 over BRPF3, whereas binding to BRD9
was weaker. Compound <b>16</b> has excellent selectivity over
nonclass IV BRD proteins. Target engagement of BRPF1B and BRPF2 with <b>16</b> was demonstrated in nanoBRET and FRAP assays. The binding
of <b>16</b> to BRPF1B was rationalized through an X-ray cocrystal
structure determination, which showed a flipped binding orientation
when compared to previous structures. We report studies that show <b>16</b> has functional activity in cellular assays by modulation
of the phenotype at low micromolar concentrations in both cancer and
inflammatory models. Pharmacokinetic data for <b>16</b> was
generated in mouse with single dose administration showing favorable
oral bioavailabilit